Magnesium in PDB 8a9t: Tubulin-[1,2]Oxazoloisoindole-1 Complex

The structure of Tubulin-[1,2]Oxazoloisoindole-1 Complex, PDB code: 8a9t was solved by A.E.Prota, A.-C.Abel, M.O.Steinmetz, P.Barraja, A.Montalbano, V.Spano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.91 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.212, 158.054, 180.717, 90, 90, 90
R / Rfree (%)	19.4 / 23.7

The structure of Tubulin-[1,2]Oxazoloisoindole-1 Complex also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Magnesium atom in the Tubulin-[1,2]Oxazoloisoindole-1 Complex (pdb code 8a9t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Tubulin-[1,2]Oxazoloisoindole-1 Complex, PDB code: 8a9t:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Tubulin-[1,2]Oxazoloisoindole-1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-[1,2]Oxazoloisoindole-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:47.5 occ:1.00 O A:HOH612 1.9 57.2 1.0 O A:HOH609 2.0 52.5 1.0 O A:HOH601 2.1 42.1 1.0 O A:HOH614 2.1 47.5 1.0 O2G A:GTP501 2.1 41.0 1.0 O1B A:GTP501 2.2 42.4 1.0 PG A:GTP501 3.1 51.2 1.0 PB A:GTP501 3.3 46.5 1.0 O3G A:GTP501 3.4 49.1 1.0 O3B A:GTP501 3.6 67.4 1.0 OE2 A:GLU71 3.8 75.8 1.0 O3A A:GTP501 3.9 53.1 1.0 OD1 A:ASP69 4.0 55.3 1.0 CG A:GLU71 4.1 64.0 1.0 NZ B:LYS254 4.2 74.9 1.0 CB A:ASP98 4.3 57.9 1.0 CB A:GLN11 4.3 49.3 1.0 OD2 A:ASP69 4.4 62.1 1.0 CD A:GLU71 4.4 69.1 1.0 OD2 A:ASP98 4.4 59.8 1.0 O1G A:GTP501 4.5 45.2 1.0 N A:GLN11 4.5 53.9 1.0 O2B A:GTP501 4.6 52.0 1.0 CG A:ASP69 4.6 53.3 1.0 CG A:ASP98 4.7 59.5 1.0 O1A A:GTP501 4.8 52.1 1.0 NE2 A:GLN11 4.8 59.6 1.0 PA A:GTP501 4.9 49.8 1.0 OG1 A:THR145 5.0 56.9 1.0 CA A:GLN11 5.0 48.6 1.0

Magnesium binding site 2 out of 4 in the Tubulin-[1,2]Oxazoloisoindole-1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-[1,2]Oxazoloisoindole-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:37.3 occ:1.00 O B:HOH609 1.9 45.9 1.0 OE1 B:GLN11 2.1 46.4 1.0 O C:HOH611 2.1 56.4 1.0 O1A B:GDP501 2.3 41.1 1.0 O B:HOH643 2.5 45.1 1.0 O B:HOH606 2.7 60.7 1.0 O B:HOH648 3.2 68.5 1.0 CD B:GLN11 3.3 57.4 1.0 PA B:GDP501 3.7 46.0 1.0 OD2 B:ASP179 3.7 62.6 1.0 CB B:GLN11 4.0 43.7 1.0 CG B:GLN11 4.1 58.0 1.0 O3A B:GDP501 4.1 48.5 1.0 NE2 B:GLN11 4.3 62.3 1.0 OE2 C:GLU254 4.3 75.4 1.0 C5' B:GDP501 4.4 47.1 1.0 OD1 B:ASN101 4.5 42.8 1.0 O5' B:GDP501 4.5 36.4 1.0 O1B B:GDP501 4.6 40.9 1.0 O2A B:GDP501 4.7 43.4 1.0 CG B:ASP179 4.8 49.6 1.0 C8 B:GDP501 4.9 50.8 1.0

Magnesium binding site 3 out of 4 in the Tubulin-[1,2]Oxazoloisoindole-1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-[1,2]Oxazoloisoindole-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:46.2 occ:1.00 O C:HOH637 2.0 41.9 1.0 O C:HOH604 2.0 46.7 1.0 O3G C:GTP501 2.0 44.9 1.0 O1B C:GTP501 2.1 39.9 1.0 O C:HOH677 2.1 40.4 1.0 O C:HOH648 2.2 40.1 1.0 PG C:GTP501 3.0 48.0 1.0 PB C:GTP501 3.1 40.7 1.0 O1G C:GTP501 3.3 41.5 1.0 O3A C:GTP501 3.5 54.0 1.0 O3B C:GTP501 3.5 54.7 1.0 OE2 C:GLU71 4.0 66.0 1.0 NZ D:LYS254 4.1 59.8 1.0 OD1 C:ASP69 4.2 49.9 1.0 CG C:GLU71 4.3 53.6 1.0 CB C:GLN11 4.4 40.9 1.0 O2G C:GTP501 4.4 41.2 1.0 OD2 C:ASP69 4.4 43.6 1.0 OD2 C:ASP98 4.4 54.0 1.0 O2B C:GTP501 4.5 50.9 1.0 CB C:ASP98 4.5 46.4 1.0 N C:GLN11 4.5 41.1 1.0 CD C:GLU71 4.6 57.2 1.0 PA C:GTP501 4.7 41.6 1.0 CG C:ASP69 4.8 55.6 1.0 OE1 C:GLN11 4.8 55.9 1.0 O1A C:GTP501 4.8 48.1 1.0 CG C:ASP98 4.9 51.6 1.0 OG1 C:THR145 4.9 45.2 1.0

Magnesium binding site 4 out of 4 in the Tubulin-[1,2]Oxazoloisoindole-1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-[1,2]Oxazoloisoindole-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:85.3 occ:1.00 O D:HOH604 1.9 67.7 1.0 OE1 D:GLN11 2.1 97.1 1.0 O1A D:GDP501 2.5 113.7 1.0 O D:HOH619 2.6 80.1 1.0 CD D:GLN11 3.0 95.2 1.0 NE2 D:GLN11 3.7 103.8 1.0 PA D:GDP501 3.9 76.6 1.0 CG D:GLN11 4.1 101.6 1.0 CB D:GLN11 4.1 79.9 1.0 O2A D:GDP501 4.3 62.1 1.0 C5' D:GDP501 4.5 72.7 1.0 C8 D:GDP501 4.7 77.7 1.0 O1B D:GDP501 4.7 76.9 1.0 O5' D:GDP501 4.8 75.7 1.0 OD1 D:ASN101 5.0 118.2 1.0

M.Barreca, V.Spano, R.Rocca, R.Bivacqua, A.C.Abel, A.Maruca, A.Montalbano, M.V.Raimondi, C.Tarantelli, E.Gaudio, L.Cascione, A.Rinaldi, R.Bai, M.O.Steinmetz, A.E.Prota, S.Alcaro, E.Hamel, F.Bertoni, P.Barraja. Development of [1,2]Oxazoloisoindoles Tubulin Polymerization Inhibitors: Further Chemical Modifications and Potential Therapeutic Effects Against Lymphomas. Eur.J.Med.Chem. V. 243 14744 2022.
ISSN: ISSN 0223-5234
PubMed: 36242921
DOI: 10.1016/J.EJMECH.2022.114744